It can depend on the actual material - but if the machine is using standard pla - then yes you can use any colour.
Stratasys are just after your money.

The eeprom reprogrammer sounds like the very first thing I would do.
If you have control of the printing temperatures in your slicer - then no you are not limited to just stratasys material.

3d printers are pretty simple beasts.
You heat stuff up and push it through a nozzle. As long as you have control over the temperatures used to 'heat stuff up' you have control ove the materials you can use.
It is that simple.